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Ejaz MR, Badr K, Hassan ZU, Al-Thani R, Jaoua S. Metagenomic approaches and opportunities in arid soil research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176173. [PMID: 39260494 DOI: 10.1016/j.scitotenv.2024.176173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/04/2024] [Accepted: 09/07/2024] [Indexed: 09/13/2024]
Abstract
Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.
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Affiliation(s)
- Muhammad Riaz Ejaz
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Kareem Badr
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Zahoor Ul Hassan
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Roda Al-Thani
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Samir Jaoua
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar.
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Suárez-Bautista JD, Manotas-Viloría HS, Leal-Mejía L, Boyacá-Vásquez J, Pineros-Castro Y, Corrales LC, Cuervo-Soto L, Vanegas J. Agricultural Biotechnological Potential of Bacillus velezensis C3-3 and Cytobacillus sp. T106 from Resource Islands of a Semi-arid Zone of La Guajira-Colombia. Curr Microbiol 2024; 81:341. [PMID: 39225835 PMCID: PMC11371855 DOI: 10.1007/s00284-024-03804-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/12/2024] [Indexed: 09/04/2024]
Abstract
Resource islands are vegetative formations in arid and semi-arid ecosystems that harbor microorganisms facing extreme conditions. However, there is a limitation in the knowledge of the agricultural biotechnological potential of microorganisms present in these islands. This study aimed to determine the capacity of Bacillus velezensis C3-3 and Cytobacillus sp. T106 isolates from resource islands to promote plant growth and control the phytopathogen Rhizoctonia solani. The bacteria were sequenced, and both grew at 50 °C, resisted 5% NaCl, withstood UV exposure, and grew in extreme pH conditions. Sixty-six genes in C3-3 and 71 in T106 were identified associated with plant growth promotion, and C3-3 was shown to promote leaf growth in lettuce plants. This promotional effect was associated with the production of indole-3-acetic acid (IAA), phosphorus solubilization, and the presence of genes related to the assimilation of rhizosphere exudates. Both strains inhibited R. solani through the production of volatile compounds and antagonism. Forty-five and 40 of these genes in C3-3 and T106, respectively, were associated with the production of proteases, lipases, siderophores, antimicrobial compounds, degradation enzymes, and secretion systems. Notably, Cytobacillus sp. has not been previously reported as a biocontrol agent. This work contributes to the evidence of the biotechnological potential of semi-arid region bacteria, offering prospects for improving agricultural production in areas with limiting conditions.
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Affiliation(s)
| | | | - Leslie Leal-Mejía
- Department of Biological Sciences, and Sustainable Processes and Products Area Faculty of Natural Sciences and Engineering, Jorge Tadeo Lozano University, Cra 4 # 22-61, Bogotá, Colombia
| | - Johanna Boyacá-Vásquez
- Department of Biology, Faculty of Sciences, Universidad Antonio Nariño, Cra. 3 Este # 47a-15, Bogotá, Colombia
| | - Yineth Pineros-Castro
- Department of Biological Sciences, and Sustainable Processes and Products Area Faculty of Natural Sciences and Engineering, Jorge Tadeo Lozano University, Cra 4 # 22-61, Bogotá, Colombia
| | - Lucia Constanza Corrales
- Colegio Mayor de Cundinamarca University, Bacteriology Program, Cl. 28, #5B-02, Bogotá, Colombia
| | - Laura Cuervo-Soto
- Department of Biology, Faculty of Sciences, Universidad Antonio Nariño, Cra. 3 Este # 47a-15, Bogotá, Colombia
| | - Javier Vanegas
- Department of Biology, Faculty of Sciences, Universidad Antonio Nariño, Cra. 3 Este # 47a-15, Bogotá, Colombia.
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3
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Muhammad M, Wahab A, Waheed A, Mohamed HI, Hakeem KR, Li L, Li WJ. Harnessing bacterial endophytes for environmental resilience and agricultural sustainability. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122201. [PMID: 39142107 DOI: 10.1016/j.jenvman.2024.122201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 08/16/2024]
Abstract
In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.
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Affiliation(s)
- Murad Muhammad
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China.
| | - Abdul Wahab
- University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
| | - Heba Ibrahim Mohamed
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, 11341, Egypt
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, 21589, Saudi Arabia; Department of Public Health, Daffodil International University, Dhaka, 1341, Bangladesh; University Centre for Research & Development, Chandigarh University, Mohali, Punjab, 140413, India
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Mousa WK, Ghemrawi R, Abu-Izneid T, Al Ramadan N, Al Sheebani F. The design and development of EcoBiomes: Multi-species synthetic microbial consortia inspired by natural desert microbiome to enhance the resilience of climate-sensitive ecosystems. Heliyon 2024; 10:e36548. [PMID: 39262988 PMCID: PMC11388679 DOI: 10.1016/j.heliyon.2024.e36548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/06/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Synthetic microbial communities, which simplify the complexity of natural ecosystems while retaining their key features, are gaining momentum in engineering and biotechnology applications. One potential application is the development of bioinoculants, offering an eco-friendly, sustainable solution to promote plant growth and increase resilience to abiotic stresses amidst climate change. A potential source for stress-tolerant microbes is those associated with desert plants, evolved and shaped by selective pressures to promote host health under harsh environmental conditions. In our research, we aim to design and develop synthetic microbial consortia inspired by the natural microbiota of four desert plants native to the Arabian Peninsula, inferred from our previous work identifying the structure and predicting the function of these microbial communities using high throughput eDNA barcoding. To obtain culturable microbes that are manageable and traceable yet still representative of natural microbial communities, we combined multiple experimental protocols coupled with compatibility and synergy assessments, along with in planta testing. We isolated a total of 75 bacteria and conducted detailed biological evaluations, revealing that an overwhelming majority (84 %) of all isolates produced indole acetic acid (IAA), with 73 % capable of solubilizing phosphate, 60 % producing siderophores, 47 % forming biofilms, and 35 % producing ACC deaminase, all contributing to plant growth and stress tolerance. We constructed four synthetic microbial consortia, named EcoBiomes, consisting of synergistic combinations of multiple species that can co-exist without significant antagonism. Our preliminary data indicate that EcoBiomes enhance the resilience of heterologous host plants under simulated environmental stresses, including drought, heat, and salinity. EcoBiomes offer a unique, sustainable, and eco-friendly solution to mitigate the impact of climate change on sensitive ecosystems, ultimately affecting global food security.
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Affiliation(s)
- Walaa K Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Tareq Abu-Izneid
- Monash Rural Health, Churchill, School of Rural Health, Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, 3844, Australia
| | - Najwa Al Ramadan
- College of Pharmacy, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Fatima Al Sheebani
- College of Pharmacy, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
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Zhang W, Liu K, Kong F, Ye T, Wang T. Multiple Functions of Compatible Solute Ectoine and Strategies for Constructing Overproducers for Biobased Production. Mol Biotechnol 2024; 66:1772-1785. [PMID: 37488320 DOI: 10.1007/s12033-023-00827-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes initially found in the hyperhalophilic bacterium Ectothiorhodospira halochloris, which inhabits the desert in Egypt. The habitat of ectoine producers implies the primary function of ectoine as a cytoprotectant against harsh conditions such as high salinity, drought, and high radiation. More extensive and in-depth studies have revealed the multiple functions of ectoine in its native producer bacterial cells and other types of cells and its biomolecular components (such as proteins and DNA) as a general protective agent. Its chemical properties as a bio-based amino acid derivative make it attractive for basic scientific research and related industries, such as the food/agricultural industry, cosmetic manufacturing, biologics, and therapeutic agent preparation. This article first discusses the functions and applications of ectoine and 5-hydroxyectoine. Subsequently, more emphasis was placed on advances in bio-based ectoine and/or 5-hydroxyectoine production. Strategies for developing more robust cell factories for highly efficient ectoine and/or 5-hydroxyectoine production are further discussed. We hope this review will provide a valuable reference for studies on the bio-based production of ectoine and 5-hydroxyectoine.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, People's Republic of China
| | - Kun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Fang Kong
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Tao Ye
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Tianwen Wang
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China.
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6
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Eckstien D, Maximov N, Margolis N, Raanan H. Towards sustainable biocontrol: inhibition of soil borne fungi by microalgae from harsh environments. Front Microbiol 2024; 15:1433765. [PMID: 39077739 PMCID: PMC11284606 DOI: 10.3389/fmicb.2024.1433765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Using microorganisms as biocontrol agents against soilborne plant pathogens is a promising alternative to chemical pesticides. However, only some biocontrol agents have proven effective under field conditions. This study explores the potential of highly resilient microalgae isolated from harsh environments, such as Biological Soil Crusts and agricultural fields in semi-arid regions, as a novel and sustainable approach to biocontrol. Fifty-nine microalgal strains, including thirteen cyanobacteria and forty-six green algae, were isolated and identified. Dual-culture plate assays and toxicity tests of microalgal growth media were conducted to evaluate the antifungal activity of the isolates against eight representative soilborne pathogens. The results showed that many microalgae strains exhibited significant inhibitory effects on the growth of specific fungal pathogens, although the activity varied among different microalgal strains and pathogen species. Some strains even promoted the growth of certain fungi. The lack of a clear pattern in the antifungal activity highlights the complexity and specificity of the interactions between microalgae and soilborne pathogens. An "Inhibition Effectiveness" metric was developed to quantify biocontrol potential based on fungal growth inhibition. The green algal genus Desmodesmus, particularly Desmodesmus subspicatus isolates, showed higher antifungal efficacy than other genera. While the inhibitory mechanisms remain unclear, the results demonstrate the promising biocontrol capabilities of microalgae from extreme environments like BSCs. Further research could unlock novel opportunities for sustainable disease management by harnessing specific microalgal strains or synergistic strain combinations targeting soilborne pathogens.
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Affiliation(s)
| | | | | | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Institute of Plant Protection, Gilat Research Center, Rishon LeTsiyon, Israel
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7
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Hong JK, Choi Y, Ahn S, Kim J, Yang DJ, Heo J, Cho JC, Lee TK. The impact of bioaerosol trajectories on microbial community assembly and physicochemical dynamics in the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172736. [PMID: 38663612 DOI: 10.1016/j.scitotenv.2024.172736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
This study explored the assembly mechanisms and physicochemical dynamics of microbial communities within atmospheric bioaerosols, focusing on the influence of different aerial trajectories. Over two years, samples near Seoul were classified into 'North', 'Southwest', and 'Others' categories based on their aerial trajectories. Physicochemical analysis of the PM2.5 particles revealed distinct ion compositions for each cluster, reflecting diverse environmental influences. Microbial community analysis revealed that shared dominant bacterial phyla were present in all clusters. However, distinct taxonomic profiles and biomarkers were also evident, such as coastal bacteria in the 'Southwest' cluster correlating with wind speed, and arid soil-originated bacteria in the 'North' cluster correlating with cations. These findings demonstrate that biomarkers in each cluster are representative of the distinct environments associated with their aerial trajectories. Notably, cluster 'Southwest' the highest microbial diversity and a strong alignment with the neutral community model, suggesting a large influence of passive dispersal from marine environments. Contrarily, 'North' and 'Others' were more influenced by niche-dependent factors. This study highlights the complex interplay between environmental factors and microbial dynamics in bioaerosols and provides important insights for environmental monitoring and public health risk assessment.
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Affiliation(s)
- Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea
| | - Yongjoo Choi
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Seokhyun Ahn
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea
| | - Jeonghwan Kim
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Dong Jin Yang
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Jongwon Heo
- Gyeonggi-do Institute of Health & Environment, Suwon, Republic of Korea
| | - Jae-Chang Cho
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea.
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Tariq A, Graciano C, Sardans J, Zeng F, Hughes AC, Ahmed Z, Ullah A, Ali S, Gao Y, Peñuelas J. Plant root mechanisms and their effects on carbon and nutrient accumulation in desert ecosystems under changes in land use and climate. THE NEW PHYTOLOGIST 2024; 242:916-934. [PMID: 38482544 DOI: 10.1111/nph.19676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
Deserts represent key carbon reservoirs, yet as these systems are threatened this has implications for biodiversity and climate change. This review focuses on how these changes affect desert ecosystems, particularly plant root systems and their impact on carbon and mineral nutrient stocks. Desert plants have diverse root architectures shaped by water acquisition strategies, affecting plant biomass and overall carbon and nutrient stocks. Climate change can disrupt desert plant communities, with droughts impacting both shallow and deep-rooted plants as groundwater levels fluctuate. Vegetation management practices, like grazing, significantly influence plant communities, soil composition, root microorganisms, biomass, and nutrient stocks. Shallow-rooted plants are particularly susceptible to climate change and human interference. To safeguard desert ecosystems, understanding root architecture and deep soil layers is crucial. Implementing strategic management practices such as reducing grazing pressure, maintaining moderate harvesting levels, and adopting moderate fertilization can help preserve plant-soil systems. Employing socio-ecological approaches for community restoration enhances carbon and nutrient retention, limits desert expansion, and reduces CO2 emissions. This review underscores the importance of investigating belowground plant processes and their role in shaping desert landscapes, emphasizing the urgent need for a comprehensive understanding of desert ecosystems.
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Affiliation(s)
- Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193, Catalonia, Spain
| | - Corina Graciano
- Instituto de Fisiología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata, 1900, Buenos Aires, Argentina
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193, Catalonia, Spain
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong, 852, China
| | - Zeeshan Ahmed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sikandar Ali
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193, Catalonia, Spain
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9
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Amenta ML, Vaccaro F, Varriale S, Sangaré JR, Defez R, Mengoni A, Bianco C. Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils. FEMS Microbiol Ecol 2024; 100:fiae041. [PMID: 38544316 PMCID: PMC11009874 DOI: 10.1093/femsec/fiae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.
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Affiliation(s)
- Maria Laura Amenta
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Francesca Vaccaro
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Stefano Varriale
- National Research Council,
Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Jean Rodrigue Sangaré
- Institut d'Economie Rurale (IER), Centre Régional de Recherche Agronomique (CRRA) de Sikasso, B.P: 16, Mali
| | - Roberto Defez
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Carmen Bianco
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
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Ben Zineb A, Lamine M, Khallef A, Hamdi H, Ahmed T, Al-Jabri H, Alsafran M, Mliki A, Sayadi S, Gargouri M. Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects. Front Microbiol 2024; 15:1362722. [PMID: 38646634 PMCID: PMC11027745 DOI: 10.3389/fmicb.2024.1362722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.
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Affiliation(s)
- Ameni Ben Zineb
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mariem Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Ahlem Khallef
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Helmi Hamdi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Hareb Al-Jabri
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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11
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Ben Gaied R, Sbissi I, Tarhouni M, Brígido C. Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium. Arch Microbiol 2024; 206:203. [PMID: 38573536 PMCID: PMC10995081 DOI: 10.1007/s00203-024-03943-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.
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Affiliation(s)
- Roukaya Ben Gaied
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal
| | - Imed Sbissi
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Mohamed Tarhouni
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Clarisse Brígido
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE-Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal.
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12
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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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14
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Islam W, Zeng F, Ahmed Dar A, Sohail Yousaf M. Dynamics of soil biota and nutrients at varied depths in a Tamarix ramosissima-dominated natural desert ecosystem: Implications for nutrient cycling and desertification management. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120217. [PMID: 38340666 DOI: 10.1016/j.jenvman.2024.120217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The underground community of soil organisms, known as soil biota, plays a critical role in terrestrial ecosystems. Different ecosystems exhibit varied responses of soil organisms to soil physical and chemical properties (SPCPs). However, our understanding of how soil biota react to different soil depths in naturally established population of salinity tolerant Tamarix ramosissima in desert ecosystems, remains limited. To address this, we employed High-Throughput Illumina HiSeq Sequencing to examine the population dynamics of soil bacteria, fungi, archaea, protists, and metazoa at six different soil depths (0-100 cm) in the naturally occurring T. ramosissima dominant zone within the Taklimakan desert of China. Our observations reveal that the alpha diversity of bacteria, fungi, metazoa, and protists displayed a linear decrease with the increase of soil depth, whereas archaea exhibited an inverse pattern. The beta diversity of soil biota, particularly metazoa, bacteria, and protists, demonstrated noteworthy associations with soil depths through Non-Metric Dimensional Scaling analysis. Among the most abundant classes of soil organisms, we observed Actinobacteria, Sordariomycetes, Halobacteria, Spirotrichea, and Nematoda for bacteria, fungi, archaea, protists, and metazoa, respectively. Additionally, we identified associations between the vertical distribution of dominant biotic communities and SPCPs. Bacterial changes were mainly influenced by total potassium, available phosphorus (AP), and soil water content (SWC), while fungi were impacted by nitrate (NO3-) and available potassium (AK). Archaea showed correlations with total carbon (TC) and AK thus suggesting their role in methanogenesis and methane oxidation, protists with AP and SWC, and metazoa with AP and pH. These correlations underscore potential connections to nutrient cycling and the production and consumption of greenhouse gases (GhGs). This insight establishes a solid foundation for devising strategies to mitigate nutrient cycling and GHG emissions in desert soils, thereby playing a pivotal role in the advancement of comprehensive approaches to sustainable desert ecosystem management.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Afzal Ahmed Dar
- Department of Building, Civil and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W. Montreal, Quebec H3G1M8, Canada
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15
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Bernacchi A, Semenzato G, di Mascolo M, Amata S, Bechini A, Berti F, Calonico C, Catania V, Emiliani G, Esposito A, Greco C, Mocali S, Mucci N, Padula A, Piccionello AP, Nasanbat B, Davaakhuu G, Bazarragchaa M, Riga F, Augugliaro C, Puglia AM, Zaccaroni M, Renato F. Antibacterial activity of Arthrobacter strains isolated from Great Gobi A Strictly Protected Area, Mongolia. AIMS Microbiol 2024; 10:161-186. [PMID: 38525036 PMCID: PMC10955175 DOI: 10.3934/microbiol.2024009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 Arthrobacter strains from topsoil samples collected from the Great Gobi A Strictly Protected Area in the Gobi Desert, were characterized by a combination of different techniques. The phylogenetic analysis, performed using their 16S rDNA sequences and the most similar Arthrobacter sequences found in databases, revealed that most of them were close to A. crystallopoietes, while others joined a sister group to the clade formed by A. humicola, A. pascens, and A. oryzae. The resistance of each strain to different antibiotics, heavy-metals, and NaCl was also tested as well as the inhibitory potential against human pathogens (i.e., Burkholderia ssp., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus ssp.) via cross-streaking, to check the production of metabolites with antimicrobial activity. Data obtained revealed that all strains were resistant to heavy metals and were able to strongly interfere with the growth of many of the human pathogens tested. The volatile organic compounds (VOCs) profile of the 11 Arthrobacter strains was also analyzed. A total of 16 different metabolites were found, some of which were already known for having an inhibitory action against different Gram-positive and Gram-negative bacteria. Isolate MS-3A13, producing the highest quantity of VOCs, is the most efficient against Burkholderia cepacia complex (Bcc), K. pneumoniae, and coagulase-negative Staphylococci (CoNS) strains. This work highlights the importance of understanding microbial populations' phenotypical characteristics and dynamics in extreme environments to uncover the antimicrobial potential of new species and strains.
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Affiliation(s)
- Alberto Bernacchi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Manuel di Mascolo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Sara Amata
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128, Palermo, Italy
| | - Angela Bechini
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Fabiola Berti
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Carmela Calonico
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Valentina Catania
- Department of Earth and Sea Science (DiSTeM), University of Palermo, Viale delle Scienze Blg. 16, Palermo, 90128, Italy
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP)—National Research Council (CNR), Via Madonna del Piano 10, Sesto Fiorentino 50019 Florence, Italy
| | - Antonia Esposito
- Council for Agricultural and Economics Research (CREA) – Agriculture and Environment, Via di Lanciola 12/A, Cascine del Riccio, 50125, Florence, Italy
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Stefano Mocali
- Council for Agricultural and Economics Research (CREA) – Agriculture and Environment, Via di Lanciola 12/A, Cascine del Riccio, 50125, Florence, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128, Palermo, Italy
| | - Battogtokh Nasanbat
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar-13330, Mongolia
| | - Gantulga Davaakhuu
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar-13330, Mongolia
| | | | - Francesco Riga
- Italian Institute for Envioronmental Protection and Research, via Vitalino Brancati, 48, 00144, Roma, Italy
| | - Claudio Augugliaro
- Wildlife Initiative, Bayangol, 6th Khoroo, Micro District 10, Ulaanbaatar, 210349, Mongolia
| | | | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Fani Renato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
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Daunoras J, Kačergius A, Gudiukaitė R. Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem. BIOLOGY 2024; 13:85. [PMID: 38392304 PMCID: PMC10886310 DOI: 10.3390/biology13020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.
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Affiliation(s)
- Jokūbas Daunoras
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
| | - Audrius Kačergius
- Lithuanian Research Centre for Agriculture and Forestry, Kedainiai Distr., LT-58344 Akademija, Lithuania
| | - Renata Gudiukaitė
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
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17
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Benitez-Alfonso Y, Soanes BK, Zimba S, Sinanaj B, German L, Sharma V, Bohra A, Kolesnikova A, Dunn JA, Martin AC, Khashi U Rahman M, Saati-Santamaría Z, García-Fraile P, Ferreira EA, Frazão LA, Cowling WA, Siddique KHM, Pandey MK, Farooq M, Varshney RK, Chapman MA, Boesch C, Daszkowska-Golec A, Foyer CH. Enhancing climate change resilience in agricultural crops. Curr Biol 2023; 33:R1246-R1261. [PMID: 38052178 DOI: 10.1016/j.cub.2023.10.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.
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Affiliation(s)
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sibongile Zimba
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK; Horticulture Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Liam German
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Anastasia Kolesnikova
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Jessica A Dunn
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Azahara C Martin
- Institute for Sustainable Agriculture (IAS-CSIC), Córdoba 14004, Spain
| | - Muhammad Khashi U Rahman
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Zaki Saati-Santamaría
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain; Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Paula García-Fraile
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Evander A Ferreira
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Leidivan A Frazão
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Wallace A Cowling
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Muhammad Farooq
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia; Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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Ramírez-Guzmán N, Torres-León C, Aguillón-Gutiérrez D, Aguirre-Joya JA. Insects, Plants, and Microorganisms from Dry Lands as Novel Sources of Proteins and Peptides for Human Consumption. Foods 2023; 12:4284. [PMID: 38231705 DOI: 10.3390/foods12234284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 01/19/2024] Open
Abstract
Protein malnutrition is present in developing countries but also in developed ones due to actual eating habits involving insufficient protein intake. In addition to this, it is estimated by the Food and Agricultural Organization of the United Nations that the world's population will increase to 9.1 billion people in less than 30 years. This poses a significant challenge in terms of nourishing the population. Different strategies have been proposed to address this challenge, including exploring novel protein sources such as plants. For instance, Prosopis alba pods have an 85.5% protein content. Other examples are microorganisms, such as Halobacillus adaensis which produces 571 U/mL of protease, and insects such as those belonging to the Orthoptera order, like grasshoppers, which have a protein content of 65.96%. These sources have been found in dry lands and are being explored to address this challenge.
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Affiliation(s)
- Nathiely Ramírez-Guzmán
- Center for Interdisciplinary Studies and Research (CEII-UAdeC), Universidad Autónoma de Coahuila, Saltillo 25280, Mexico
| | - Cristian Torres-León
- Reaserch Center and Ethnobiological Garden (CIJE), Universidad Autónoma de Coahuila, Viesca 27480, Mexico
| | - David Aguillón-Gutiérrez
- Reaserch Center and Ethnobiological Garden (CIJE), Universidad Autónoma de Coahuila, Viesca 27480, Mexico
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Zhu YL, Huang YJ, Nuerhamanti N, Bai XY, Wang HN, Zhu XY, Zhang W. The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere. MICROBIAL ECOLOGY 2023; 87:2. [PMID: 38008827 DOI: 10.1007/s00248-023-02320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/25/2023] [Indexed: 11/28/2023]
Abstract
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.
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Affiliation(s)
- Yan-Lei Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
| | - Yong-Jie Huang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Naifeisai Nuerhamanti
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Xiao-Yu Bai
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Hui-Nan Wang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Xiao-Ying Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
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20
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Zhu YL, Huang YJ, Nuerhamanti N, Bai XY, Wang HN, Zhu XY, Zhang W. Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere. MICROBIAL ECOLOGY 2023; 86:2461-2476. [PMID: 37301781 DOI: 10.1007/s00248-023-02252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.
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Affiliation(s)
- Yan-Lei Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
| | - Yong-Jie Huang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Naifeisai Nuerhamanti
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Xiao-Yu Bai
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Hui-Nan Wang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Xiao-Ying Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
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21
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Damavandi MS, Shojaei H, Esfahani BN. The anticancer and antibacterial potential of bioactive secondary metabolites derived From bacterial endophytes in association with Artemisia absinthium. Sci Rep 2023; 13:18473. [PMID: 37891400 PMCID: PMC10611800 DOI: 10.1038/s41598-023-45910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
The continuous search for secondary metabolites in microorganisms isolated from untapped reservoirs is an effective prospective approach to drug discovery. In this study, an in-depth analysis was conducted to investigate the diversity of culturable bacterial endophytes present in the medicinal plant A. absinthium, as well as the antibacterial and anticancer potential of their bioactive secondary metabolites. The endophytic bacteria recovered from A. absinthium, were characterized via the implementation of suitable biochemical and molecular analyses. Agar well diffusion and broth microdilution were used to screen antibacterial activity. SEM was performed to assess the impact of the extracted metabolite on MRSA strain cell morphology. Apoptosis and cytotoxicity assays were used to evaluate anticancer activity against MCF7 and A549. The FTIR, GC-MS were used to detect bioactive compounds in the active solvent fraction. Of the various endophytic bacteria studied, P. aeruginosa SD01 showed discernible activity against both bacterial pathogens and malignancies. The crude ethyl acetate extract of P. aeruginosa SD01 showed MICs of 32 and 128 µg/mL for S. aureus and MRSA, respectively. SEM examination demonstrated MRSA bacterial cell lysis, hole development, and intracellular leaking. This study revealed that the crude bioactive secondary metabolite SD01 has potent anticancer activity. In this study, 2-aminoacetophenone, 1,2-apyrazine-1,4-dione, phenazine and 2-phenyl-4-cyanopyridine were the major bioactive secondary metabolites. In conclusion, our findings indicate that the bacteria recovered from A. absinthium plants and in particular, P. aeruginosa SD01 is a remarkable source of untapped therapeutic, i.e., antimicrobial and anticancer compounds.
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Affiliation(s)
- Mohammad Sadegh Damavandi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hasan Shojaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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22
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Chavarria-Quicaño E, Contreras-Jácquez V, Carrillo-Fasio A, De la Torre-González F, Asaff-Torres A. Native Bacillus paralicheniformis isolate as a potential agent for phytopathogenic nematodes control. Front Microbiol 2023; 14:1213306. [PMID: 37588888 PMCID: PMC10425774 DOI: 10.3389/fmicb.2023.1213306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Phytopathogenic nematodes (PPNs) are responsible for substantial damages within agricultural crops worldwide which can be controlled employing beneficial microorganisms and/or their metabolites in an ecofriendly way. Nevertheless, the success of the control regards not only on the virulence of the strains or the toxicity of their metabolites but also on their ability to colonize and remain in the rhizospheric environment, particularly in those crops affected by abiotic stresses promoted by the climate change. Consequently, the bioprospection of beneficial microorganisms able to control PPNs and to thrive in adverse conditions has attracted attention. On this way, deserts are perfect ecological niches to isolate microorganisms adapted to harsh enviroments. The purpose of this research was to isolate and characterize bacteria from rhizospheric soil samples collected in the Northwestern Desert of Mexico with potential for PPNs control. As first screening, secretomes of each isolate were tested in vitro for nematicidal activity (NA). Then, activities from secretomes and endospores from the selected isolate were confirmed in vivo assays. From 100 thermotolerant isolates, the secretome of the isolate identified as Bacillus paralicheniformis TB197 showed the highest NA (>95%) against Meloidogyne incognita, both in vitro and in vivo tests, suppressing infections caused by M. enterolobii in tomato crops, too. In open field tests, the endospores of TB197 strain showed a reduction of 81% in the infection severity caused by M. enterolobii (p ≤ 0.05), while the galling index (GI) was reduced 84% (p ≤ 0.05) in tomato greenhouse-tests. Also, a reduction of the root necrosis (81%) caused by Radopholus similis in banana plantations (p ≤ 0.05), compared to the control was observed. Owing to their efficacy in controlling PPNs infections, the endospores and secondary metabolites of B. paralicheniformis TB197 strain could be used in bionematicidal formulations.
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Affiliation(s)
- Estefany Chavarria-Quicaño
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Victor Contreras-Jácquez
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Armando Carrillo-Fasio
- Laboratory of Nematology, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Mexico
| | | | - Ali Asaff-Torres
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
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23
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Contreras MJ, Leal K, Bruna P, Nuñez-Montero K, Goméz-Espinoza O, Santos A, Bravo L, Valenzuela B, Solis F, Gahona G, Cayo M, Dinamarca MA, Ibacache-Quiroga C, Zamorano P, Barrientos L. Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities. Front Microbiol 2023; 14:1197399. [PMID: 37538842 PMCID: PMC10395097 DOI: 10.3389/fmicb.2023.1197399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.
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Affiliation(s)
- María José Contreras
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Pablo Bruna
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Kattia Nuñez-Montero
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
- Biotechnology Research Center, Instituto Tecnológico de Costa Rica, Cártago, Costa Rica
| | - Olman Goméz-Espinoza
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Universitat Autònoma de Barcelona, Departament de Genètica i de Microbiologia, Institut Biotecnologia i de Biomedicina, Cerdanyola del Vallès, Barcelona, Spain
| | - León Bravo
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Giovanni Gahona
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Mayra Cayo
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Leticia Barrientos
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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25
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Anand S, Hallsworth JE, Timmis J, Verstraete W, Casadevall A, Ramos JL, Sood U, Kumar R, Hira P, Dogra Rawat C, Kumar A, Lal S, Lal R, Timmis K. Weaponising microbes for peace. Microb Biotechnol 2023; 16:1091-1111. [PMID: 36880421 PMCID: PMC10221547 DOI: 10.1111/1751-7915.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.
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Affiliation(s)
- Shailly Anand
- Department of ZoologyDeen Dayal Upadhyaya College, University of DelhiDelhiIndia
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - James Timmis
- Athena Institute for Research on Innovation and Communication in Health and Life SciencesVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
| | - Arturo Casadevall
- Department of MedicineJohns Hopkins School of Public Health and School of MedicineBaltimoreMarylandUSA
| | | | - Utkarsh Sood
- Department of ZoologyKirori Mal College, University of DelhiDelhiIndia
| | - Roshan Kumar
- Post‐Graduate Department of ZoologyMagadh UniversityBodh GayaBiharIndia
| | - Princy Hira
- Department of ZoologyMaitreyi College, University of DelhiNew DelhiIndia
| | | | - Abhilash Kumar
- Department of ZoologyRamjas College, University of DelhiDelhiIndia
| | - Sukanya Lal
- PhiXgen Pvt. LtdGurugram, GurgaonHaryanaIndia
| | - Rup Lal
- Acharya Narendra Dev College, University of DelhiGovindpuri, Kalkaji, New DelhiIndia
| | - Kenneth Timmis
- Institute of Microbiology, Technical University BraunschweigBraunschweigGermany
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26
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Segaran TC, Azra MN, Lananan F, Wang Y. Microbe, climate change and marine environment: Linking trends and research hotspots. MARINE ENVIRONMENTAL RESEARCH 2023:106015. [PMID: 37291004 DOI: 10.1016/j.marenvres.2023.106015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 06/10/2023]
Abstract
Microbes, or microorganisms, have been the foundation of the biosphere for over 3 billion years and have played an essential role in shaping our planet. The available knowledge on the topic of microbes associated with climate change has the potential to reshape upcoming research trends globally. As climate change impacts the ocean or marine ecosystem, the responses of these "unseen life" will heavily influence the achievement of a sustainable evolutionary environment. The present study aims to identify microbial-related research under changing climate within the marine environment through the mapping of visualized graphs of the available literature. We used scientometric methods to retrieve documents from the Web of Science platform in the Core Collection (WOSCC) database, analyzing a total of 2767 documents based on scientometric indicators. Our findings show that this research area is growing exponentially, with the most influential keywords being "microbial diversity," "bacteria," and "ocean acidification," and the most cited being "microorganism" and "diversity." The identification of influential clusters in the field of marine science provides insight into the hot spots and frontiers of research in this area. Prominent clusters include "coral microbiome," "hypoxic zone," "novel Thermoplasmatota clade," "marine dinoflagellate bloom," and "human health." Analyzing emerging trends and transformative changes in this field can inform the creation of special issues or research topics in selected journals, thus increasing visibility and engagement among the scientific community.
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Affiliation(s)
- Thirukanthan Chandra Segaran
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Mohamad Nor Azra
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia; Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Organization, National Research and Innovation Agency (BRIN), Pemenang, West Nusa Tenggara, 83352, Indonesia.
| | - Fathurrahman Lananan
- East Coast Environmental Research Institute, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia.
| | - Youji Wang
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.
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González F, Santander C, Ruiz A, Pérez R, Moreira J, Vidal G, Aroca R, Santos C, Cornejo P. Inoculation with Actinobacteria spp. Isolated from a Hyper-Arid Environment Enhances Tolerance to Salinity in Lettuce Plants ( Lactuca sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2018. [PMID: 37653935 PMCID: PMC10222102 DOI: 10.3390/plants12102018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 08/31/2023]
Abstract
Irrigated agriculture is responsible for a third of global agricultural production, but the overuse of water resources and intensification of farming practices threaten its sustainability. The use of saline water in irrigation has become an alternative in areas subjected to frequent drought, but this practice affects plant growth due to osmotic impact and excess of ions. Plant-growth-promoting rhizobacteria (PGPR) can mitigate the negative impacts of salinity and other abiotic factors on crop yields. Actinobacteria from the hyper-arid Atacama Desert could increase the plant tolerance to salinity, allowing their use as biofertilizers for lettuce crops using waters with high salt contents. In this work, rhizosphere samples of halophytic Metharme lanata were obtained from Atacama Desert, and actinobacteria were isolated and identified by 16S gene sequencing. The PGPR activities of phosphate solubilization, nitrogen fixation, and the production of siderophore and auxin were assessed at increasing concentrations of NaCl, as well as the enhancement of salt tolerance in lettuce plants irrigated with 100 mM of NaCl. Photosynthesis activity and chlorophyll content, proline content, lipid peroxidation, cation and P concentration, and the identification and quantification of phenolic compounds were assessed. The strains S. niveoruber ATMLC132021 and S. lienomycini ATMLC122021 were positive for nitrogen fixation and P solubilization activities and produced auxin up to 200 mM NaCl. In lettuce plants, both strains were able to improve salt stress tolerance by increasing proline contents, carotenoids, chlorophyll, water use efficiency (WUE), stomatal conductance (gs), and net photosynthesis (A), concomitantly with the overproduction of the phenolic compound dicaffeoylquinic acid. All these traits were positively correlated with the biomass production under saltwater irrigation, suggesting its possible use as bioinoculants for the agriculture in areas where the water resources are scarce and usually with high salt concentrations.
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Affiliation(s)
- Felipe González
- Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile;
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
| | - Christian Santander
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
- Grupo de Ingeniería Ambiental y Biotecnología, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción 4070411, Chile;
| | - Antonieta Ruiz
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
| | - Rodrigo Pérez
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
| | - Jorge Moreira
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
| | - Gladys Vidal
- Grupo de Ingeniería Ambiental y Biotecnología, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción 4070411, Chile;
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain;
| | - Cledir Santos
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (A.R.); (R.P.); (J.M.); (C.S.)
| | - Pablo Cornejo
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile
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Sengupta P, Sivabalan SKM, Mahesh A, Palanikumar I, Kuppa Baskaran DK, Raman K. Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes. J Indian Inst Sci 2023; 103:1-17. [PMID: 37362854 PMCID: PMC10073628 DOI: 10.1007/s41745-023-00370-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/05/2023] [Indexed: 06/28/2023]
Abstract
Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.
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Affiliation(s)
- Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | | | - Amrita Mahesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Indumathi Palanikumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
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Matthews A, Lima-Zaloumis J, Debes Ii RV, Boyer G, Trembath-Reichert E. Heterotrophic Growth Dominates in the Most Extremotolerant Extremophile Cultures. ASTROBIOLOGY 2023; 23:446-459. [PMID: 36723486 DOI: 10.1089/ast.2022.0100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Due to their ability to withstand "extreme" conditions, Earth's extremophilic organisms can constrain habitability windows for other planetary systems. However, there are many other considerations to microbial growth requirements beyond environmental extremes, such as nutrient availability. Here, we conduct a literature review of the most extremotolerant extremophiles in culture, since working with cultured organisms allows environmental and nutrient variables to be constrained with a high level of specificity. We generated a database that includes the isolation environment, carbon source(s) used, and growth preferences across temperature, pressure, salinity, and pH extremes. We found that the "most extreme" conditions were primarily sustained by heterotrophs, except for hyperthermophiles. These results highlight the importance of considering organic carbon availability when using extremophiles for habitability constraints. We also interrogated polyextreme potential across temperature, pressure, salinity, and pH conditions. Our findings suggest that the investigation of growth tolerance rather than growth optimum may reveal wider habitability parameters. Overall, these results highlight the potential polyextremes, environments, nutrient requirements, and additional analyses that could improve the application of cultured investigations to astrobiology questions.
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Affiliation(s)
- Adrianna Matthews
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | | | - R Vincent Debes Ii
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Grayson Boyer
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
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Zuo Y, He C, Zhang D, Zhao L, He X, Sun X. Soil variables driven by host plant and growth season affect soil microbial composition and metabolism in extremely arid desert ecosystems. Microbiol Res 2023; 269:127315. [PMID: 36738491 DOI: 10.1016/j.micres.2023.127315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 11/27/2022] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Assessment changes of soil microbial community structure and function is important in understanding the response to desert ecosystem management. In present study, variations of soil microbial community and edaphic factors associated with five desert shrubs were determined in Anxi extremely arid desert in Northwest China in growing (summer), deciduous (autumn), and snowfall (winter) seasons. For that, the microbial composition and catabolic metabolism were examined using methods of phospholipid fatty acid (PLFA) and Biolog EcoPlate, respectively. Regardless of plant species and seasonal patterns, the microbial community was mostly dominated by gram-negative bacteria (GN); and the carbohydrates, amino acids and polymers were the main carbon sources for desert microbial metabolism. Microbial biomass and metabolic levels were significantly higher in both summer and winter than those of autumn. There was no correlation between soil microbial community and carbon utilization in winter; but GN was positively correlated with metabolism of amines carbon sources in summer, while fungal community presented the strongest correlation with suites of carbon sources' metabolic levels in autumn, indicating the uncoupled relationship between microbial community and function in desert ecosystems. Desert shrubs significantly influenced the composition of soil microbial community, whereas the variation of microbial catabolic metabolism was most attributed to seasonality. Nevertheless, the effects of both plant species (21.3 %) and climate variation (84.9 %) interacted with soil properties, indicating the seasonality of soil nutrients predominately determined the changes in composition and metabolism of desert microbes. Both the comprehensive seasonal level and the intra-seasonal paired correlation analysis proved that phosphorus was the key factor in determining microbial community composition, while ammonia and nitrate nitrogen were more correlated to microbial functional metabolism. Additionally, soil moisture and organic carbon in desert environment also induced the shifts in ratio of fungi and bacterial communities. We conclude that the seasonal patterns of soil microbial community and metabolic function in extremely arid desert are predictable, and mainly influenced by specific soil factors driven by desert shrubs and climate factors. These findings will provide a basis for evaluating the management of soil resources and microbial function in desert environments.
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Affiliation(s)
- Yiling Zuo
- School of Life Sciences, Hebei University, Baoding 071002, China; College of Traditional Chinese Medicine, Hebei University, Baoding 071002, China.
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Dongdong Zhang
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Lili Zhao
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xueli He
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xiang Sun
- School of Life Sciences, Hebei University, Baoding 071002, China.
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Draft Genome Sequences of Three Pseudomonas chengduensis Strains Isolated from Desert Soil in Morocco. Microbiol Resour Announc 2023; 12:e0108222. [PMID: 36633413 PMCID: PMC9933653 DOI: 10.1128/mra.01082-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We report the draft genome sequences of three Pseudomonas chengduensis strains isolated from the sand dunes of the Merzouga (MDMC17 strain) and Erg Lihoudi (MDMC216 and MDMC224 strains) regions in the Moroccan desert. These bacteria are able to tolerate the harsh environmental conditions of the desert ecosystem.
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32
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Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study. Arch Microbiol 2023; 205:90. [PMID: 36780035 DOI: 10.1007/s00203-023-03432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.
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Blilou I, Hirt H. Desert plants to stop desertification: To succeed, reforestation projects to reclaim once fertile lands need to consider the local abiotic, biotic, and social factors: To succeed, reforestation projects to reclaim once fertile lands need to consider the local abiotic, biotic, and social factors. EMBO Rep 2023; 24:e56687. [PMID: 36579758 PMCID: PMC9900327 DOI: 10.15252/embr.202256687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding the intricate relationship between plants, desert soils, and desert-specific microbiomes would increase the success chances for reforestation projects to reclaim lands lost to desertification.
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Affiliation(s)
- Ikram Blilou
- Center for Desert AgricultureKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Heribert Hirt
- Center for Desert AgricultureKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Zhang Z, Chai X, Gao Y, Zhang B, Lu Y, Du Y, Zhang Y, Ding Y, Tariq A, Ullah A, Li X, Zeng F. Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages. Microorganisms 2022; 10:microorganisms10122376. [PMID: 36557629 PMCID: PMC9785364 DOI: 10.3390/microorganisms10122376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- Correspondence: (Z.Z.); (F.Z.)
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yi Du
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Ya Ding
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.Z.); (F.Z.)
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Procter M, Kundu B, Sudalaimuthuasari N, AlMaskari RS, Saeed EE, Hazzouri KM, Amiri KMA. Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria. Microorganisms 2022; 10:microorganisms10102083. [PMID: 36296358 PMCID: PMC9607294 DOI: 10.3390/microorganisms10102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications.
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Affiliation(s)
- Miranda Procter
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Raja S. AlMaskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Esam E. Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
| | - Khaled M. A. Amiri
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
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Wang J, Qu M, Wang Y, He N, Li J. Plant traits and community composition drive the assembly processes of abundant and rare fungi across deserts. Front Microbiol 2022; 13:996305. [PMID: 36246243 PMCID: PMC9554466 DOI: 10.3389/fmicb.2022.996305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022] Open
Abstract
The difference in community assembly mechanisms between rare and abundant fungi in deserts remains unknown. Hence, we compared the distribution patterns of abundant and rare fungi, and assessed the factors driving their assembly mechanisms across major vegetation types (shrubby desert, semi-shrubby and dwarf semi-shrubby desert, dwarf semi-arboreous desert, and shrubby steppe desert) of Chinese deserts. We assessed abundant and rare fungal subcommunities base on the sequencing data of fungal ITS data. Abundant fungal assembly was more affected by neutral processes than the rare. Null model and VPA analysis indicated that heterogeneous selection dominated rare sub-communities, whereas abundant fungal assembly was mainly determined by heterogeneous selection, dispersal limitation and other, unknown processes together. As a result, abundant sub-communities exhibited a higher species turnover rate than the rare. Hierarchical partitioning analysis indicated that soil conditions and plant attributes drove the assembly processes of abundant and rare fungi, respectively. Meanwhile, the relative strength of different assembly processes differed significantly among four vegetation types. In addition, we found that plant functional traits and composition played more critical roles in shaping the assembly processes of rare fungi than those of abundant fungi. Taken together, our findings collectively suggest that rare and abundant fungi exhibit differential ecological patterns that are driven by distinct assembly processes in deserts. We emphasize that the assembly processes of abundant and rare fungi are dependent on different abiotic and biotic factors in desert ecosystems.
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Affiliation(s)
- Jianming Wang
- School of Ecology Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mengjun Qu
- School of Ecology Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yin Wang
- School of Ecology Nature Conservation, Beijing Forestry University, Beijing, China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Jingwen Li
- School of Ecology Nature Conservation, Beijing Forestry University, Beijing, China
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Loganathachetti DS, Alhashmi F, Chandran S, Mundra S. Irrigation water salinity structures the bacterial communities of date palm ( Phoenix dactylifera)-associated bulk soil. FRONTIERS IN PLANT SCIENCE 2022; 13:944637. [PMID: 35991423 PMCID: PMC9388049 DOI: 10.3389/fpls.2022.944637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The irrigation of date palms (Phoenix dactylifera) with saline groundwater is routinely practiced in the agroecosystems of arid environments because of freshwater scarcity. This leads to salts deposition in topsoil layers and increases soil salinization. However, how different irrigation sources affect soil microbiota is poorly understood. Bulk soil samples were collected from date farms receiving non-saline water and saline groundwater to examine bacterial communities using metabarcoding. Overall, bacterial diversity measures (Shannon diversity index, richness, and evenness) did not vary between irrigation sources. Bacterial communities were structured based on irrigation water sources and were significantly associated with their electrical conductivity. Of 5,155 operational taxonomic units (OTUs), 21.3% were unique to soil irrigated with saline groundwater, 31.5% received non-saline water irrigation, and 47.2% were shared. The Proteobacteria abundance was higher in soil under saline groundwater irrigation while Actinobacteriota abundance was lower. A compositional shift at the genera level was also evident; the abundance of Subgroup_10 and Mycobacterium was higher under saline groundwater irrigation. Mycobacterium was a key indicator of OTU under saline groundwater irrigation while Solirubrobacter was an indicator of non-saline water irrigation. Functional gene analyses showed enrichment of fatty acid, cell wall, and starch biosynthesis pathways in soil under saline groundwater irrigation. These findings provide insights into how "salinity filtering" influences bacterial communities, key taxa, and the potential metabolic function in soil under increasing irrigation water salinities, and have broad implications for arid agroecosystems.
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Affiliation(s)
| | - Fardous Alhashmi
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
| | - Subha Chandran
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
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38
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Feng L, Dong T, Jiang P, Yang Z, Dong A, Xie SQ, Griffin CH, Wu R. An eco-evo-devo genetic network model of stress response. HORTICULTURE RESEARCH 2022; 9:uhac135. [PMID: 36061617 PMCID: PMC9433980 DOI: 10.1093/hr/uhac135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/04/2022] [Indexed: 05/23/2023]
Abstract
The capacity of plants to resist abiotic stresses is of great importance to agricultural, ecological and environmental sustainability, but little is known about its genetic underpinnings. Existing genetic tools can identify individual genetic variants mediating biochemical, physiological, and cellular defenses, but fail to chart an overall genetic atlas behind stress resistance. We view stress response as an eco-evo-devo process by which plants adaptively respond to stress through complex interactions of developmental canalization, phenotypic plasticity, and phenotypic integration. As such, we define and quantify stress response as the developmental change of adaptive traits from stress-free to stress-exposed environments. We integrate composite functional mapping and evolutionary game theory to reconstruct omnigenic, information-flow interaction networks for stress response. Using desert-adapted Euphrates poplar as an example, we infer salt resistance-related genome-wide interactome networks and trace the roadmap of how each SNP acts and interacts with any other possible SNPs to mediate salt resistance. We characterize the previously unknown regulatory mechanisms driving trait variation; i.e. the significance of a SNP may be due to the promotion of positive regulators, whereas the insignificance of a SNP may result from the inhibition of negative regulators. The regulator-regulatee interactions detected are not only experimentally validated by two complementary experiments, but also biologically interpreted by their encoded protein-protein interactions. Our eco-evo-devo model of genetic interactome networks provides an approach to interrogate the genetic architecture of stress response and informs precise gene editing for improving plants' capacity to live in stress environments.
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Affiliation(s)
| | | | | | - Zhenyu Yang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Christopher H Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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Marasco R, Fusi M, Ramond JB, Van Goethem MW, Seferji K, Maggs-Kölling G, Cowan DA, Daffonchio D. The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition. ISME COMMUNICATIONS 2022; 2:47. [PMID: 37938683 PMCID: PMC9723607 DOI: 10.1038/s43705-022-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 06/17/2023]
Abstract
Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kholoud Seferji
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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Behairi S, Baha N, Barakat M, Ortet P, Achouak W, Heulin T, Kaci Y. Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil. Extremophiles 2022; 26:18. [PMID: 35652980 DOI: 10.1007/s00792-022-01268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/05/2022] [Indexed: 11/04/2022]
Abstract
Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.
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Affiliation(s)
- Sabrina Behairi
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Nassima Baha
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Mohamed Barakat
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Yahia Kaci
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria.
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Xiao J, Lan S, Zhang Z, Yang L, Qian L, Xia L, Song S, Farías ME, Torres RM, Wu L. Physical Disturbance Reduces Cyanobacterial Relative Abundance and Substrate Metabolism Potential of Biological Soil Crusts on a Gold Mine Tailing of Central China. Front Microbiol 2022; 13:811039. [PMID: 35464943 PMCID: PMC9019783 DOI: 10.3389/fmicb.2022.811039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
As the critical ecological engineers, biological soil crusts (biocrusts) are considered to play essential roles in improving substrate conditions during ecological rehabilitation processes. Physical disturbance, however, often leads to the degradation of biocrusts, and it remains unclear how the physical disturbance affects biocrust microorganisms and their related metabolism. In this study, the photosynthetic biomass (indicated by chlorophyll a), nutrients, enzyme activities, and bacterial communities of biocrusts were investigated in a gold mine tailing of Central China to evaluate the impact of physical disturbance on biocrusts during the rehabilitation process of gold mine tailings. The results show that physical disturbance significantly reduced the photosynthetic biomass, nutrient contents (organic carbon, ammonium nitrogen, nitrate nitrogen, and total phosphorus), and enzyme activities (β-glucosidase, sucrase, nitrogenase, neutral phosphatase, and urease) of biocrusts in the mine tailings. Furthermore, 16S rDNA sequencing showed that physical disturbance strongly changed the composition, structure, and interactions of the bacterial community, leading to a shift from a cyanobacteria dominated community to a heterotrophic bacteria (proteobacteria, actinobacteria, and acidobacteria) dominated community and a more complex bacterial network (higher complexity, nodes, and edges). Altogether, our results show that the biocrusts dominated by cyanobacteria could also develop in the tailings of humid region, and the dominants (e.g., Microcoleus) were the same as those from dryland biocrusts; nevertheless, physical disturbance significantly reduced cyanobacterial relative abundance in biocrusts. Based on our findings, we propose the future work on cyanobacterial inoculation (e.g., Microcoleus), which is expected to promote substrate metabolism and accumulation, ultimately accelerating the development of biocrusts and the subsequent ecological restoration of tailings.
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Affiliation(s)
- Jingshang Xiao
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zulin Zhang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China.,The James Hutton Institute, Aberdeen, United Kingdom
| | - Lie Yang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Long Qian
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Ling Xia
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Shaoxian Song
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Centro Científico Tecnológico (CCT), Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Rosa María Torres
- CETMIC- CONICET- CCT La Plata, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), La Plata, Argentina
| | - Li Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
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42
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Kochhar N, I․K K, Shrivastava S, Ghosh A, Rawat VS, Sodhi KK, Kumar M. Perspectives on the microorganism of extreme environments and their applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100134. [PMID: 35909612 PMCID: PMC9325743 DOI: 10.1016/j.crmicr.2022.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Extremophiles are organisms that can survive and thrive in conditions termed as "extreme" by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.
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Affiliation(s)
- Nikita Kochhar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | - Kavya I․K
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Anshika Ghosh
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Kushneet Kaur Sodhi
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Mohit Kumar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
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43
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Analytic Hierarchy Process Based Land Suitability for Organic Farming in the Arid Region. SUSTAINABILITY 2022. [DOI: 10.3390/su14084542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The use of organic farming in the Thar desert region (great Indian desert) is extremely low due to the low humidity and high temperatures across India. As a result, the desert area faces significant challenges in agricultural production and in meeting the demand for high-quality food. Thus, the farming community in this area needs to expand to meet the required demands. Geospatial technologies are capable of recommending suitable farming areas in desert regions and, specifically, to increase organic farming. However, the prevalence of organic farming is very low in developing countries. In this study, a multi-criteria decision-making process was used to determine land suitability for organic crops and to increase organic food production. This study attempted to identify suitable land for reliable organic farming in Rajasthan’s Barmer district. The analytical hierarchy process (AHP) technique combined with the geographic information system approach showed that, in the Barmer district, the highly suitable area for organic farming comprises about 832 sq. km and the moderately suitable area covers about 8524 sq. km. Monthly Gravity Recovery and Climate Experiment (GRACE) and precipitation data were used to identify the impact of organic farming in the Barmer district for the period from January 2017 to December 2020. Finally, this study investigated the quality of land and its application so that it can be used effectively to solve social and economic problems.
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44
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Parihar J, Parihar SP, Suravajhala P, Bagaria A. Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert. BIOLOGY 2022; 11:biology11030461. [PMID: 35336834 PMCID: PMC8945486 DOI: 10.3390/biology11030461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary We present a systematic investigation of the distribution of microbial communities in arid and semi-arid regions of Thar Desert Rajasthan, India. Their responses in multiple environmental stresses, including surface soil, surface water and underground water were evaluated. We further assess the biotechnological potential of native microorganisms and discover functional species with results providing a detailed understanding of the abundance of microbial communities in these regions, associated with various stress-related biogeochemical and biotechnological processes. We hope our work will facilitate the development of effective future strategies for the use of extremophiles in complex environments. Abstract The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications.
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Affiliation(s)
- Jagdish Parihar
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
| | - Suraj P Parihar
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Prashanth Suravajhala
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Amritapuri Campus, Clappana P.O., Kollam 690525, India
| | - Ashima Bagaria
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
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Coleine C, Delgado-Baquerizo M, Albanese D, Singh BK, Stajich JE, Selbmann L, Egidi E. Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth. FEMS Microbiol Ecol 2022; 98:6550019. [PMID: 35298630 DOI: 10.1093/femsec/fiac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/05/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semi-arid drylands. We show that rocks support a consistent and unique mycobiome that was different to that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes, and Eurotiomycetes. In addition, comparing to soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach, 1, 38098 S. Michele all'Adige (TN), Italy
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California-Riverside, Riverside, CA, 92521, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
| | - Eleonora Egidi
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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46
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Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem. Sci Rep 2022; 12:3741. [PMID: 35260670 PMCID: PMC8904503 DOI: 10.1038/s41598-022-07765-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.
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Coban O, De Deyn GB, van der Ploeg M. Soil microbiota as game-changers in restoration of degraded lands. Science 2022; 375:abe0725. [PMID: 35239372 DOI: 10.1126/science.abe0725] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Land degradation reduces soil functioning and, consequently, the services that soil provides. Soil hydrological functions are critical to combat soil degradation and promote soil restoration. Soil microorganisms affect soil hydrology, but the role of soil microbiota in forming and sustaining soil is not well explored. Case studies indicate the potential of soil microorganisms as game-changers in restoring soil functions. We review the state of the art of microorganism use in land restoration technology, the groups of microorganisms with the greatest potential for soil restoration, knowledge of the effect of microorganisms on soil physical properties, and proposed strategies for the long-term restoration of degraded lands. We also emphasize the need to advance the emerging research field of biophysical landscape interactions to support soil-plant ecosystem restoration practices.
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Affiliation(s)
- Oksana Coban
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Gerlinde B De Deyn
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Martine van der Ploeg
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
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Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
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Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano. DIVERSITY 2021. [DOI: 10.3390/d14010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth.
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Zvinavashe AT, Mardad I, Mhada M, Kouisni L, Marelli B. Engineering the Plant Microenvironment To Facilitate Plant-Growth-Promoting Microbe Association. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13270-13285. [PMID: 33929839 DOI: 10.1021/acs.jafc.1c00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New technologies that enhance soil biodiversity and minimize the use of scarce resources while boosting crop production are highly sought to mitigate the increasing threats that climate change, population growth, and desertification pose on the food infrastructure. In particular, solutions based on plant-growth-promoting bacteria (PGPB) bring merits of self-replication, low environmental impact, tolerance to biotic and abiotic stressors, and reduction of inputs, such as fertilizers. However, challenges in facilitating PGPB delivery in the soil still persist and include survival to desiccation, precise delivery, programmable resuscitation, competition with the indigenous rhizosphere, and soil structure. These factors play a critical role in microbial root association and development of a beneficial plant microbiome. Engineering the seed microenvironment with protein and polysaccharides is one proposed way to deliver PGPB precisely and effectively in the seed spermosphere. In this review, we will cover new advancements in the precise and scalable delivery of microbial inoculants, also highlighting the latest development of multifunctional rhizobacteria solutions that have beneficial impact on not only legumes but also cereals. To conclude, we will discuss the role that legislators and policymakers play in promoting the adoption of new technologies that can enhance the sustainability of crop production.
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Affiliation(s)
- Augustine T Zvinavashe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ilham Mardad
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
| | - Manal Mhada
- African integrated Plant and Soil Group (AiPlaS), AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
| | - Lamfeddal Kouisni
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University (ASARI-UM6P), 70000 Laayoune, Morocco
| | - Benedetto Marelli
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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